Multiple sequence alignment - TraesCS1D01G215300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1D01G215300 chr1D 100.000 3268 0 0 1 3268 300709979 300706712 0.000000e+00 6035.0
1 TraesCS1D01G215300 chr1D 95.219 502 19 4 2766 3263 282972231 282971731 0.000000e+00 789.0
2 TraesCS1D01G215300 chr1D 92.308 39 3 0 164 202 65905158 65905120 4.560000e-04 56.5
3 TraesCS1D01G215300 chr1B 89.895 2375 110 43 338 2680 405712524 405710248 0.000000e+00 2937.0
4 TraesCS1D01G215300 chr1B 95.600 500 19 3 2766 3265 12600680 12600184 0.000000e+00 798.0
5 TraesCS1D01G215300 chr1B 95.219 502 19 5 2766 3265 670051337 670050839 0.000000e+00 789.0
6 TraesCS1D01G215300 chr1B 94.303 509 23 6 2758 3265 40950109 40950612 0.000000e+00 774.0
7 TraesCS1D01G215300 chr1A 92.166 1570 65 22 1 1543 375017294 375015756 0.000000e+00 2165.0
8 TraesCS1D01G215300 chr1A 94.986 1037 28 15 1569 2594 375015769 375014746 0.000000e+00 1605.0
9 TraesCS1D01G215300 chr1A 89.730 185 15 4 2579 2762 375014732 375014551 1.960000e-57 233.0
10 TraesCS1D01G215300 chr7D 95.418 502 20 3 2766 3265 472740401 472740901 0.000000e+00 797.0
11 TraesCS1D01G215300 chr7D 77.957 186 39 2 117 300 390470804 390470989 7.410000e-22 115.0
12 TraesCS1D01G215300 chr4B 95.000 500 22 3 2766 3265 5024994 5025490 0.000000e+00 782.0
13 TraesCS1D01G215300 chr6D 94.810 501 24 2 2766 3266 293606144 293606642 0.000000e+00 780.0
14 TraesCS1D01G215300 chr6D 85.256 156 23 0 1673 1828 15640547 15640702 9.380000e-36 161.0
15 TraesCS1D01G215300 chr3D 94.821 502 23 3 2765 3265 612599590 612600089 0.000000e+00 780.0
16 TraesCS1D01G215300 chr4D 94.810 501 21 5 2766 3265 348414654 348415150 0.000000e+00 776.0
17 TraesCS1D01G215300 chr3A 81.437 167 29 2 112 277 163177138 163177303 5.690000e-28 135.0
18 TraesCS1D01G215300 chr3A 84.536 97 11 4 114 208 515827581 515827487 3.470000e-15 93.5
19 TraesCS1D01G215300 chrUn 80.380 158 25 4 108 263 18060103 18059950 7.410000e-22 115.0
20 TraesCS1D01G215300 chrUn 88.312 77 9 0 1735 1811 12882458 12882382 3.470000e-15 93.5
21 TraesCS1D01G215300 chr2B 83.478 115 18 1 101 214 788023491 788023605 4.460000e-19 106.0
22 TraesCS1D01G215300 chr5D 81.522 92 15 2 115 204 370360109 370360200 1.260000e-09 75.0
23 TraesCS1D01G215300 chr5B 94.872 39 2 0 164 202 121004822 121004860 9.790000e-06 62.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G215300 chr1D 300706712 300709979 3267 True 6035.000000 6035 100.000 1 3268 1 chr1D.!!$R3 3267
1 TraesCS1D01G215300 chr1D 282971731 282972231 500 True 789.000000 789 95.219 2766 3263 1 chr1D.!!$R2 497
2 TraesCS1D01G215300 chr1B 405710248 405712524 2276 True 2937.000000 2937 89.895 338 2680 1 chr1B.!!$R2 2342
3 TraesCS1D01G215300 chr1B 40950109 40950612 503 False 774.000000 774 94.303 2758 3265 1 chr1B.!!$F1 507
4 TraesCS1D01G215300 chr1A 375014551 375017294 2743 True 1334.333333 2165 92.294 1 2762 3 chr1A.!!$R1 2761
5 TraesCS1D01G215300 chr7D 472740401 472740901 500 False 797.000000 797 95.418 2766 3265 1 chr7D.!!$F2 499

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
903 927 0.31812 ACTTCATTTTTGCCCGCTGG 59.682 50.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2409 2472 0.466189 GCTGCCCATGCTAAAGCCTA 60.466 55.0 0.0 0.0 41.18 3.93 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 7.764695 TTCTATTTTAGCGACGAATTGATGA 57.235 32.000 0.00 0.00 0.00 2.92
45 46 7.946655 TCTATTTTAGCGACGAATTGATGAT 57.053 32.000 0.00 0.00 0.00 2.45
54 55 7.733608 AGCGACGAATTGATGATATGATTTAC 58.266 34.615 0.00 0.00 0.00 2.01
71 72 7.316687 TGATTTACGAATCTAATAACGCTCG 57.683 36.000 0.00 0.00 41.80 5.03
75 76 4.665212 ACGAATCTAATAACGCTCGAACA 58.335 39.130 0.00 0.00 0.00 3.18
77 78 4.733887 CGAATCTAATAACGCTCGAACACT 59.266 41.667 0.00 0.00 0.00 3.55
78 79 5.330866 CGAATCTAATAACGCTCGAACACTG 60.331 44.000 0.00 0.00 0.00 3.66
89 90 1.346395 TCGAACACTGGGTGTAAGCAT 59.654 47.619 3.69 0.00 46.79 3.79
106 107 3.004024 GCATAGGGCAAATCGAATGTG 57.996 47.619 0.00 0.00 43.97 3.21
108 109 3.548818 GCATAGGGCAAATCGAATGTGTC 60.549 47.826 0.00 0.00 43.97 3.67
110 111 1.173043 GGGCAAATCGAATGTGTCCA 58.827 50.000 11.02 0.00 37.00 4.02
121 122 3.578688 GAATGTGTCCAATGGCAAGTTC 58.421 45.455 0.00 1.33 0.00 3.01
123 124 1.955778 TGTGTCCAATGGCAAGTTCAG 59.044 47.619 0.00 0.00 0.00 3.02
130 131 0.534877 ATGGCAAGTTCAGTGACGCA 60.535 50.000 0.00 0.00 0.00 5.24
133 134 0.937304 GCAAGTTCAGTGACGCAAGA 59.063 50.000 0.00 0.00 43.62 3.02
141 142 3.402110 TCAGTGACGCAAGAATGACAAT 58.598 40.909 0.00 0.00 43.62 2.71
143 144 4.275689 TCAGTGACGCAAGAATGACAATTT 59.724 37.500 0.00 0.00 43.62 1.82
146 147 6.636447 CAGTGACGCAAGAATGACAATTTTAA 59.364 34.615 0.00 0.00 43.62 1.52
150 151 7.116090 TGACGCAAGAATGACAATTTTAATTGG 59.884 33.333 16.96 2.82 45.04 3.16
151 152 6.928492 ACGCAAGAATGACAATTTTAATTGGT 59.072 30.769 16.96 5.44 45.04 3.67
214 216 1.944032 ACCGTGTGTGTCAACTAACC 58.056 50.000 0.00 0.00 0.00 2.85
218 220 2.933906 CGTGTGTGTCAACTAACCTGTT 59.066 45.455 0.00 0.00 0.00 3.16
219 221 3.242284 CGTGTGTGTCAACTAACCTGTTG 60.242 47.826 0.00 0.00 46.09 3.33
239 241 7.065324 CCTGTTGTTCTTGTGTCACTAAACTTA 59.935 37.037 4.27 0.00 0.00 2.24
272 275 2.078849 TCGATTTGTGATGTGCTCGT 57.921 45.000 0.00 0.00 0.00 4.18
274 277 2.921121 TCGATTTGTGATGTGCTCGTAC 59.079 45.455 0.00 0.00 0.00 3.67
275 278 2.029244 CGATTTGTGATGTGCTCGTACC 59.971 50.000 0.00 0.00 0.00 3.34
277 280 3.945981 TTTGTGATGTGCTCGTACCTA 57.054 42.857 0.00 0.00 0.00 3.08
299 302 7.091443 CCTAACGTCAGATAGGTATCATTTCC 58.909 42.308 3.28 0.00 37.90 3.13
315 318 6.882610 TCATTTCCGATGATTTATCTTGGG 57.117 37.500 0.00 1.70 33.44 4.12
317 320 6.486657 TCATTTCCGATGATTTATCTTGGGTC 59.513 38.462 6.57 0.00 33.49 4.46
577 582 1.667724 GAACATGCGTCAGAATCAGGG 59.332 52.381 0.00 0.00 0.00 4.45
807 819 1.500474 TCCTCCATGATTCGCTCCTT 58.500 50.000 0.00 0.00 0.00 3.36
808 820 1.139654 TCCTCCATGATTCGCTCCTTG 59.860 52.381 0.00 0.00 0.00 3.61
890 914 1.375523 GTCGCCGTTCCCACTTCAT 60.376 57.895 0.00 0.00 0.00 2.57
899 923 0.965439 TCCCACTTCATTTTTGCCCG 59.035 50.000 0.00 0.00 0.00 6.13
903 927 0.318120 ACTTCATTTTTGCCCGCTGG 59.682 50.000 0.00 0.00 0.00 4.85
964 988 2.513026 ATCAGACCACAGCTGCCGAC 62.513 60.000 15.27 4.24 33.45 4.79
1023 1047 2.825836 CGGGTCTCTGCCAATGCC 60.826 66.667 0.00 0.00 36.33 4.40
1243 1267 2.663520 CCGGCGGCGCATGTTATA 60.664 61.111 34.36 0.00 0.00 0.98
1244 1268 2.248135 CCGGCGGCGCATGTTATAA 61.248 57.895 34.36 0.00 0.00 0.98
1245 1269 1.083015 CGGCGGCGCATGTTATAAC 60.083 57.895 34.36 11.63 0.00 1.89
1246 1270 1.083015 GGCGGCGCATGTTATAACG 60.083 57.895 34.36 0.25 0.00 3.18
1247 1271 1.639534 GCGGCGCATGTTATAACGT 59.360 52.632 29.21 7.81 0.00 3.99
1248 1272 0.027063 GCGGCGCATGTTATAACGTT 59.973 50.000 29.21 5.88 0.00 3.99
1249 1273 1.258458 GCGGCGCATGTTATAACGTTA 59.742 47.619 29.21 11.02 0.00 3.18
1250 1274 2.882876 CGGCGCATGTTATAACGTTAC 58.117 47.619 10.81 0.92 0.00 2.50
1251 1275 2.282026 CGGCGCATGTTATAACGTTACA 59.718 45.455 10.81 7.54 0.00 2.41
1252 1276 3.600346 GGCGCATGTTATAACGTTACAC 58.400 45.455 10.81 10.97 0.00 2.90
1260 1284 6.171932 TGTTATAACGTTACACAATGCCAG 57.828 37.500 10.81 0.00 0.00 4.85
1545 1590 0.682209 ATACGTGGGTAGCAGTCCGT 60.682 55.000 0.00 0.00 30.81 4.69
1546 1591 0.035534 TACGTGGGTAGCAGTCCGTA 60.036 55.000 0.00 0.00 0.00 4.02
1549 1594 0.604578 GTGGGTAGCAGTCCGTAACA 59.395 55.000 0.00 0.00 0.00 2.41
1550 1595 1.206371 GTGGGTAGCAGTCCGTAACAT 59.794 52.381 0.00 0.00 0.00 2.71
1551 1596 1.206132 TGGGTAGCAGTCCGTAACATG 59.794 52.381 0.00 0.00 0.00 3.21
1552 1597 1.206371 GGGTAGCAGTCCGTAACATGT 59.794 52.381 0.00 0.00 0.00 3.21
1553 1598 2.354403 GGGTAGCAGTCCGTAACATGTT 60.354 50.000 16.68 16.68 0.00 2.71
1554 1599 3.119029 GGGTAGCAGTCCGTAACATGTTA 60.119 47.826 14.35 14.35 0.00 2.41
1555 1600 3.861689 GGTAGCAGTCCGTAACATGTTAC 59.138 47.826 30.61 30.61 41.37 2.50
1556 1601 3.955650 AGCAGTCCGTAACATGTTACT 57.044 42.857 34.33 21.86 42.31 2.24
1557 1602 3.846360 AGCAGTCCGTAACATGTTACTC 58.154 45.455 34.33 25.93 42.31 2.59
1558 1603 3.510360 AGCAGTCCGTAACATGTTACTCT 59.490 43.478 34.33 27.18 42.31 3.24
1559 1604 3.612860 GCAGTCCGTAACATGTTACTCTG 59.387 47.826 34.33 33.10 42.31 3.35
1560 1605 4.806330 CAGTCCGTAACATGTTACTCTGT 58.194 43.478 34.33 20.02 42.31 3.41
1561 1606 5.620654 GCAGTCCGTAACATGTTACTCTGTA 60.621 44.000 33.76 21.52 42.31 2.74
1562 1607 6.384224 CAGTCCGTAACATGTTACTCTGTAA 58.616 40.000 34.33 17.24 42.31 2.41
1563 1608 7.033791 CAGTCCGTAACATGTTACTCTGTAAT 58.966 38.462 34.33 17.92 42.31 1.89
1564 1609 8.186163 CAGTCCGTAACATGTTACTCTGTAATA 58.814 37.037 34.33 15.38 42.31 0.98
1565 1610 8.404000 AGTCCGTAACATGTTACTCTGTAATAG 58.596 37.037 34.33 20.80 42.31 1.73
1566 1611 8.186821 GTCCGTAACATGTTACTCTGTAATAGT 58.813 37.037 34.33 4.88 42.31 2.12
1567 1612 8.186163 TCCGTAACATGTTACTCTGTAATAGTG 58.814 37.037 34.33 19.85 42.31 2.74
1568 1613 7.043590 CCGTAACATGTTACTCTGTAATAGTGC 60.044 40.741 34.33 12.95 42.31 4.40
1569 1614 6.887376 AACATGTTACTCTGTAATAGTGCG 57.113 37.500 9.97 0.00 0.00 5.34
1570 1615 5.962433 ACATGTTACTCTGTAATAGTGCGT 58.038 37.500 0.00 0.00 0.00 5.24
1571 1616 5.805486 ACATGTTACTCTGTAATAGTGCGTG 59.195 40.000 0.00 0.00 0.00 5.34
1572 1617 4.740268 TGTTACTCTGTAATAGTGCGTGG 58.260 43.478 0.00 0.00 0.00 4.94
1573 1618 2.961526 ACTCTGTAATAGTGCGTGGG 57.038 50.000 0.00 0.00 0.00 4.61
1574 1619 2.176889 ACTCTGTAATAGTGCGTGGGT 58.823 47.619 0.00 0.00 0.00 4.51
1575 1620 3.359033 ACTCTGTAATAGTGCGTGGGTA 58.641 45.455 0.00 0.00 0.00 3.69
1577 1622 2.100252 TCTGTAATAGTGCGTGGGTAGC 59.900 50.000 0.00 0.00 0.00 3.58
1591 1636 0.179124 GGTAGCAGTCTCGGCTCAAG 60.179 60.000 0.00 0.00 42.62 3.02
1602 1647 3.882888 TCTCGGCTCAAGAAAACATGTTT 59.117 39.130 18.13 18.13 0.00 2.83
1603 1648 5.049680 GTCTCGGCTCAAGAAAACATGTTTA 60.050 40.000 23.53 7.36 31.63 2.01
1604 1649 5.049680 TCTCGGCTCAAGAAAACATGTTTAC 60.050 40.000 23.53 7.84 31.63 2.01
1605 1650 3.906008 CGGCTCAAGAAAACATGTTTACG 59.094 43.478 23.53 12.33 31.63 3.18
1606 1651 4.553938 CGGCTCAAGAAAACATGTTTACGT 60.554 41.667 23.53 8.96 31.63 3.57
1607 1652 4.675114 GGCTCAAGAAAACATGTTTACGTG 59.325 41.667 23.53 19.22 38.76 4.49
1609 1654 6.423862 GCTCAAGAAAACATGTTTACGTGTA 58.576 36.000 23.53 7.88 44.64 2.90
1740 1785 2.247358 CCTGTGGCCAAGTACCATTTT 58.753 47.619 7.24 0.00 39.95 1.82
1842 1887 1.796459 CAGTTCCAAAGGTCCGTAACG 59.204 52.381 0.00 0.00 0.00 3.18
1884 1933 3.057456 CACAGTAGTACTCCAAGCGAACT 60.057 47.826 0.00 0.00 0.00 3.01
1895 1954 2.436824 GCGAACTCTTGGGGCTCC 60.437 66.667 0.00 0.00 0.00 4.70
1915 1974 0.179124 GGTCACTGATCAGCTCCGTC 60.179 60.000 22.83 6.67 0.00 4.79
1961 2020 0.462047 ATCATCCGGGCTTGAACGTC 60.462 55.000 0.00 0.00 0.00 4.34
2372 2433 6.032094 ACTGTCAAGGTATATGTTTACGTCG 58.968 40.000 0.00 0.00 0.00 5.12
2409 2472 3.753272 CGAAGATGTGTTGGAATGGAAGT 59.247 43.478 0.00 0.00 0.00 3.01
2429 2492 2.053865 GGCTTTAGCATGGGCAGCA 61.054 57.895 3.88 0.00 44.61 4.41
2479 2542 4.525024 GGCTTCTGTCTAGTGGAGTAGTA 58.475 47.826 0.00 0.00 0.00 1.82
2480 2543 4.577283 GGCTTCTGTCTAGTGGAGTAGTAG 59.423 50.000 0.00 0.00 34.23 2.57
2481 2544 5.187687 GCTTCTGTCTAGTGGAGTAGTAGT 58.812 45.833 0.00 0.00 34.51 2.73
2634 2726 8.099364 TCATTTCTAAAAGTCCTAGTTTGCAG 57.901 34.615 0.00 0.00 0.00 4.41
2659 2751 5.753744 TGGTGAATTAACGTTGTGACATTC 58.246 37.500 11.99 10.64 0.00 2.67
2688 2781 9.535878 TTTTTAAAATACAGAGGCAAACGATTT 57.464 25.926 0.55 0.00 0.00 2.17
2689 2782 8.514136 TTTAAAATACAGAGGCAAACGATTTG 57.486 30.769 0.00 0.00 43.44 2.32
2722 2815 0.034863 GGATGCCGGTAAGTCCCAAA 60.035 55.000 1.90 0.00 0.00 3.28
2738 2831 1.604755 CCAAACGTTCGGGATTTGACA 59.395 47.619 12.34 0.00 35.73 3.58
2742 2835 1.810151 ACGTTCGGGATTTGACAATGG 59.190 47.619 0.00 0.00 0.00 3.16
2747 2840 4.513198 TCGGGATTTGACAATGGAAAAC 57.487 40.909 0.00 0.00 0.00 2.43
2748 2841 3.257127 TCGGGATTTGACAATGGAAAACC 59.743 43.478 0.00 0.00 0.00 3.27
2749 2842 3.616317 CGGGATTTGACAATGGAAAACCC 60.616 47.826 12.40 12.40 39.60 4.11
2800 2893 5.254032 AGAGAGGGATTTGGTGGAATAGTTT 59.746 40.000 0.00 0.00 0.00 2.66
2820 2915 7.232118 AGTTTTTATGTATTGCTTGAGCCTT 57.768 32.000 0.00 0.00 41.18 4.35
2997 3095 4.681978 AGGCAAGCCGACGGACAC 62.682 66.667 20.50 0.00 41.95 3.67
3142 3242 3.066190 CCGTGGTCGAGGTAGCCA 61.066 66.667 0.00 0.00 39.71 4.75
3146 3246 1.987306 TGGTCGAGGTAGCCATGCA 60.987 57.895 0.00 0.00 0.00 3.96
3188 3288 4.682334 TCGGGGTAGCCGGTGTCA 62.682 66.667 17.03 0.00 0.00 3.58
3265 3366 0.032952 GGTGTCGAAGTAGTGGTGCA 59.967 55.000 0.00 0.00 0.00 4.57
3266 3367 1.337823 GGTGTCGAAGTAGTGGTGCAT 60.338 52.381 0.00 0.00 0.00 3.96
3267 3368 1.993370 GTGTCGAAGTAGTGGTGCATC 59.007 52.381 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 9.058424 CGAGCGTTATTAGATTCGTAAATCATA 57.942 33.333 1.41 0.00 43.21 2.15
54 55 4.733887 AGTGTTCGAGCGTTATTAGATTCG 59.266 41.667 0.00 0.00 0.00 3.34
61 62 1.001633 ACCCAGTGTTCGAGCGTTATT 59.998 47.619 0.00 0.00 0.00 1.40
71 72 3.270877 CCTATGCTTACACCCAGTGTTC 58.729 50.000 5.59 0.00 45.08 3.18
75 76 0.546598 GCCCTATGCTTACACCCAGT 59.453 55.000 0.00 0.00 36.87 4.00
77 78 0.995803 TTGCCCTATGCTTACACCCA 59.004 50.000 0.00 0.00 42.00 4.51
78 79 2.137810 TTTGCCCTATGCTTACACCC 57.862 50.000 0.00 0.00 42.00 4.61
89 90 2.026729 TGGACACATTCGATTTGCCCTA 60.027 45.455 0.00 0.00 0.00 3.53
97 98 2.127271 TGCCATTGGACACATTCGAT 57.873 45.000 6.95 0.00 0.00 3.59
98 99 1.811965 CTTGCCATTGGACACATTCGA 59.188 47.619 6.95 0.00 0.00 3.71
106 107 2.030805 GTCACTGAACTTGCCATTGGAC 60.031 50.000 6.95 0.00 0.00 4.02
108 109 1.069022 CGTCACTGAACTTGCCATTGG 60.069 52.381 0.00 0.00 0.00 3.16
110 111 0.593128 GCGTCACTGAACTTGCCATT 59.407 50.000 0.00 0.00 0.00 3.16
121 122 3.818961 ATTGTCATTCTTGCGTCACTG 57.181 42.857 0.00 0.00 0.00 3.66
123 124 6.984740 TTAAAATTGTCATTCTTGCGTCAC 57.015 33.333 0.00 0.00 0.00 3.67
141 142 9.715121 ACGAAGTAGACATCTTACCAATTAAAA 57.285 29.630 0.00 0.00 41.94 1.52
143 144 7.277098 GCACGAAGTAGACATCTTACCAATTAA 59.723 37.037 0.00 0.00 41.61 1.40
146 147 5.105310 AGCACGAAGTAGACATCTTACCAAT 60.105 40.000 0.00 0.00 41.61 3.16
150 151 7.028361 ACTAAAGCACGAAGTAGACATCTTAC 58.972 38.462 0.00 0.00 41.61 2.34
151 152 7.154435 ACTAAAGCACGAAGTAGACATCTTA 57.846 36.000 0.00 0.00 41.61 2.10
155 156 8.773404 AATAAACTAAAGCACGAAGTAGACAT 57.227 30.769 0.00 0.00 41.61 3.06
156 157 8.597662 AAATAAACTAAAGCACGAAGTAGACA 57.402 30.769 0.00 0.00 41.61 3.41
157 158 9.874215 AAAAATAAACTAAAGCACGAAGTAGAC 57.126 29.630 0.00 0.00 41.61 2.59
158 159 9.872757 CAAAAATAAACTAAAGCACGAAGTAGA 57.127 29.630 0.00 0.00 41.61 2.59
197 199 2.546778 ACAGGTTAGTTGACACACACG 58.453 47.619 0.00 0.00 0.00 4.49
214 216 6.422776 AGTTTAGTGACACAAGAACAACAG 57.577 37.500 8.59 0.00 0.00 3.16
218 220 8.902540 ATGATAAGTTTAGTGACACAAGAACA 57.097 30.769 8.59 0.00 0.00 3.18
250 252 2.762472 GAGCACATCACAAATCGAACG 58.238 47.619 0.00 0.00 0.00 3.95
251 253 2.157668 ACGAGCACATCACAAATCGAAC 59.842 45.455 0.00 0.00 34.46 3.95
252 254 2.412870 ACGAGCACATCACAAATCGAA 58.587 42.857 0.00 0.00 34.46 3.71
254 256 2.029244 GGTACGAGCACATCACAAATCG 59.971 50.000 0.00 0.00 36.32 3.34
255 257 3.262420 AGGTACGAGCACATCACAAATC 58.738 45.455 0.00 0.00 0.00 2.17
274 277 7.091443 GGAAATGATACCTATCTGACGTTAGG 58.909 42.308 7.57 8.42 40.74 2.69
275 278 6.802348 CGGAAATGATACCTATCTGACGTTAG 59.198 42.308 0.00 0.00 33.88 2.34
277 280 5.301045 TCGGAAATGATACCTATCTGACGTT 59.699 40.000 0.00 0.00 33.88 3.99
288 291 8.454106 CCAAGATAAATCATCGGAAATGATACC 58.546 37.037 1.22 0.00 37.75 2.73
289 292 8.454106 CCCAAGATAAATCATCGGAAATGATAC 58.546 37.037 1.22 0.00 37.75 2.24
296 299 4.165180 TGGACCCAAGATAAATCATCGGAA 59.835 41.667 0.00 0.00 38.81 4.30
299 302 6.701340 TCTATGGACCCAAGATAAATCATCG 58.299 40.000 0.00 0.00 38.81 3.84
315 318 0.753262 ACCGTCATGCCTCTATGGAC 59.247 55.000 0.00 0.00 38.35 4.02
317 320 0.250038 CCACCGTCATGCCTCTATGG 60.250 60.000 0.00 0.00 39.35 2.74
577 582 2.380084 TGGATCAAACCTCACGCTAC 57.620 50.000 0.00 0.00 0.00 3.58
635 647 4.026156 CGCAAGTGACGCAAATCG 57.974 55.556 0.00 0.00 45.38 3.34
808 820 1.669999 GGTCACATGGGCAATGGCTC 61.670 60.000 6.84 0.00 40.94 4.70
814 826 0.403655 TAGCAAGGTCACATGGGCAA 59.596 50.000 0.00 0.00 0.00 4.52
899 923 1.539157 GATTTATAGGGCAGGCCAGC 58.461 55.000 16.94 12.53 37.98 4.85
903 927 0.039764 GGGGGATTTATAGGGCAGGC 59.960 60.000 0.00 0.00 0.00 4.85
964 988 6.026947 AGCCAGTAGTACTTGTCAAGTAAG 57.973 41.667 23.80 12.78 44.95 2.34
1077 1101 1.805945 GGTGTAGTTGAGCGCCGAG 60.806 63.158 2.29 0.00 0.00 4.63
1081 1105 3.488090 GCCGGTGTAGTTGAGCGC 61.488 66.667 1.90 0.00 33.03 5.92
1239 1263 4.938832 AGCTGGCATTGTGTAACGTTATAA 59.061 37.500 11.86 8.01 42.39 0.98
1241 1265 3.343617 AGCTGGCATTGTGTAACGTTAT 58.656 40.909 11.86 0.00 42.39 1.89
1242 1266 2.773487 AGCTGGCATTGTGTAACGTTA 58.227 42.857 3.29 3.29 42.39 3.18
1243 1267 1.604604 AGCTGGCATTGTGTAACGTT 58.395 45.000 5.88 5.88 42.39 3.99
1244 1268 1.604604 AAGCTGGCATTGTGTAACGT 58.395 45.000 0.00 0.00 42.39 3.99
1245 1269 2.095853 CCTAAGCTGGCATTGTGTAACG 59.904 50.000 0.00 0.00 42.39 3.18
1246 1270 3.343617 TCCTAAGCTGGCATTGTGTAAC 58.656 45.455 0.00 0.00 37.35 2.50
1247 1271 3.712016 TCCTAAGCTGGCATTGTGTAA 57.288 42.857 0.00 0.00 0.00 2.41
1248 1272 3.931907 ATCCTAAGCTGGCATTGTGTA 57.068 42.857 0.00 0.00 0.00 2.90
1249 1273 2.814805 ATCCTAAGCTGGCATTGTGT 57.185 45.000 0.00 0.00 0.00 3.72
1250 1274 3.813443 ACTATCCTAAGCTGGCATTGTG 58.187 45.455 0.00 0.00 0.00 3.33
1251 1275 4.510167 AACTATCCTAAGCTGGCATTGT 57.490 40.909 0.00 0.00 0.00 2.71
1252 1276 8.507249 GTTATTAACTATCCTAAGCTGGCATTG 58.493 37.037 0.00 0.00 0.00 2.82
1260 1284 9.472361 TCGACATTGTTATTAACTATCCTAAGC 57.528 33.333 7.99 0.00 0.00 3.09
1435 1477 3.068585 CGTCGGCGCTGTAGTATAC 57.931 57.895 17.37 4.68 43.42 1.47
1457 1499 8.841300 TGACTAATCTAGTGTAATGACTAGCAG 58.159 37.037 0.00 0.00 43.57 4.24
1545 1590 7.486870 CACGCACTATTACAGAGTAACATGTTA 59.513 37.037 14.35 14.35 0.00 2.41
1546 1591 6.310467 CACGCACTATTACAGAGTAACATGTT 59.690 38.462 16.68 16.68 0.00 2.71
1549 1594 5.348986 CCACGCACTATTACAGAGTAACAT 58.651 41.667 0.00 0.00 0.00 2.71
1550 1595 4.381185 CCCACGCACTATTACAGAGTAACA 60.381 45.833 0.00 0.00 0.00 2.41
1551 1596 4.110482 CCCACGCACTATTACAGAGTAAC 58.890 47.826 0.00 0.00 0.00 2.50
1552 1597 3.765511 ACCCACGCACTATTACAGAGTAA 59.234 43.478 0.00 0.00 0.00 2.24
1553 1598 3.359033 ACCCACGCACTATTACAGAGTA 58.641 45.455 0.00 0.00 0.00 2.59
1554 1599 2.176889 ACCCACGCACTATTACAGAGT 58.823 47.619 0.00 0.00 0.00 3.24
1555 1600 2.961526 ACCCACGCACTATTACAGAG 57.038 50.000 0.00 0.00 0.00 3.35
1556 1601 2.100252 GCTACCCACGCACTATTACAGA 59.900 50.000 0.00 0.00 0.00 3.41
1557 1602 2.159156 TGCTACCCACGCACTATTACAG 60.159 50.000 0.00 0.00 31.40 2.74
1558 1603 1.826096 TGCTACCCACGCACTATTACA 59.174 47.619 0.00 0.00 31.40 2.41
1559 1604 2.159142 ACTGCTACCCACGCACTATTAC 60.159 50.000 0.00 0.00 33.19 1.89
1560 1605 2.100252 GACTGCTACCCACGCACTATTA 59.900 50.000 0.00 0.00 33.19 0.98
1561 1606 0.902531 ACTGCTACCCACGCACTATT 59.097 50.000 0.00 0.00 33.19 1.73
1562 1607 0.460311 GACTGCTACCCACGCACTAT 59.540 55.000 0.00 0.00 33.19 2.12
1563 1608 0.611062 AGACTGCTACCCACGCACTA 60.611 55.000 0.00 0.00 33.19 2.74
1564 1609 1.878656 GAGACTGCTACCCACGCACT 61.879 60.000 0.00 0.00 33.19 4.40
1565 1610 1.446272 GAGACTGCTACCCACGCAC 60.446 63.158 0.00 0.00 33.19 5.34
1566 1611 2.970639 GAGACTGCTACCCACGCA 59.029 61.111 0.00 0.00 35.80 5.24
1567 1612 2.202623 CGAGACTGCTACCCACGC 60.203 66.667 0.00 0.00 0.00 5.34
1568 1613 2.490217 CCGAGACTGCTACCCACG 59.510 66.667 0.00 0.00 0.00 4.94
1569 1614 2.184579 GCCGAGACTGCTACCCAC 59.815 66.667 0.00 0.00 0.00 4.61
1570 1615 2.037367 AGCCGAGACTGCTACCCA 59.963 61.111 0.00 0.00 37.28 4.51
1571 1616 1.605058 TTGAGCCGAGACTGCTACCC 61.605 60.000 0.00 0.00 39.69 3.69
1572 1617 0.179124 CTTGAGCCGAGACTGCTACC 60.179 60.000 0.00 0.00 39.69 3.18
1573 1618 0.811915 TCTTGAGCCGAGACTGCTAC 59.188 55.000 0.00 0.00 39.69 3.58
1574 1619 1.545841 TTCTTGAGCCGAGACTGCTA 58.454 50.000 0.00 0.00 39.69 3.49
1575 1620 0.681733 TTTCTTGAGCCGAGACTGCT 59.318 50.000 0.00 0.00 43.03 4.24
1577 1622 2.483876 TGTTTTCTTGAGCCGAGACTG 58.516 47.619 0.00 0.00 0.00 3.51
1591 1636 6.788930 GCTACACTACACGTAAACATGTTTTC 59.211 38.462 27.66 21.25 34.23 2.29
1602 1647 2.925578 AATGCGCTACACTACACGTA 57.074 45.000 9.73 0.00 0.00 3.57
1603 1648 2.163010 ACTAATGCGCTACACTACACGT 59.837 45.455 9.73 0.00 0.00 4.49
1604 1649 2.793933 ACTAATGCGCTACACTACACG 58.206 47.619 9.73 0.00 0.00 4.49
1605 1650 4.031426 GTCAACTAATGCGCTACACTACAC 59.969 45.833 9.73 0.00 0.00 2.90
1606 1651 4.082408 AGTCAACTAATGCGCTACACTACA 60.082 41.667 9.73 0.00 0.00 2.74
1607 1652 4.421948 AGTCAACTAATGCGCTACACTAC 58.578 43.478 9.73 0.00 0.00 2.73
1608 1653 4.713824 AGTCAACTAATGCGCTACACTA 57.286 40.909 9.73 0.00 0.00 2.74
1609 1654 3.594603 AGTCAACTAATGCGCTACACT 57.405 42.857 9.73 0.00 0.00 3.55
1842 1887 1.230324 GTCAAGGTTGTGCCAGAGAC 58.770 55.000 0.00 0.00 40.61 3.36
1884 1933 3.319198 GTGACCGGAGCCCCAAGA 61.319 66.667 9.46 0.00 0.00 3.02
1895 1954 1.226802 CGGAGCTGATCAGTGACCG 60.227 63.158 27.97 27.97 35.65 4.79
1961 2020 2.372690 CCGCTCGACGTGGAAGTTG 61.373 63.158 0.86 0.00 46.58 3.16
2311 2370 3.550820 ACTTTGCATTCACACTGTACCA 58.449 40.909 0.00 0.00 0.00 3.25
2351 2410 5.170270 CGACGACGTAAACATATACCTTGAC 59.830 44.000 0.00 0.00 34.56 3.18
2394 2455 3.073274 AGCCTACTTCCATTCCAACAC 57.927 47.619 0.00 0.00 0.00 3.32
2409 2472 0.466189 GCTGCCCATGCTAAAGCCTA 60.466 55.000 0.00 0.00 41.18 3.93
2479 2542 1.112113 CTGGGTAGCACGTGGATACT 58.888 55.000 18.88 8.18 38.44 2.12
2480 2543 3.661745 CTGGGTAGCACGTGGATAC 57.338 57.895 18.88 10.83 37.65 2.24
2634 2726 4.911053 TGTCACAACGTTAATTCACCAAC 58.089 39.130 0.00 0.00 0.00 3.77
2683 2776 3.316029 TCCCTAATGAATGCAGCAAATCG 59.684 43.478 0.00 0.00 0.00 3.34
2684 2777 4.924305 TCCCTAATGAATGCAGCAAATC 57.076 40.909 0.00 1.41 0.00 2.17
2685 2778 4.502604 GCATCCCTAATGAATGCAGCAAAT 60.503 41.667 0.00 0.00 37.59 2.32
2688 2781 1.958579 GCATCCCTAATGAATGCAGCA 59.041 47.619 0.00 0.00 37.59 4.41
2689 2782 1.271656 GGCATCCCTAATGAATGCAGC 59.728 52.381 8.61 0.00 39.78 5.25
2691 2784 1.608055 CGGCATCCCTAATGAATGCA 58.392 50.000 8.61 0.00 39.78 3.96
2692 2785 0.883833 CCGGCATCCCTAATGAATGC 59.116 55.000 0.00 0.00 37.59 3.56
2693 2786 2.276732 ACCGGCATCCCTAATGAATG 57.723 50.000 0.00 0.00 37.59 2.67
2694 2787 3.394606 ACTTACCGGCATCCCTAATGAAT 59.605 43.478 0.00 0.00 37.59 2.57
2695 2788 2.775384 ACTTACCGGCATCCCTAATGAA 59.225 45.455 0.00 0.00 37.59 2.57
2722 2815 1.810151 CCATTGTCAAATCCCGAACGT 59.190 47.619 0.00 0.00 0.00 3.99
2764 2857 3.390175 TCCCTCTCTCCCTTCTAACAG 57.610 52.381 0.00 0.00 0.00 3.16
2800 2893 5.105797 CCACAAGGCTCAAGCAATACATAAA 60.106 40.000 4.13 0.00 44.36 1.40
2820 2915 5.818887 TGTACTCCTATATATACGCCCACA 58.181 41.667 0.00 0.00 0.00 4.17
3146 3246 1.086696 CATCGACCACGGCATTCTTT 58.913 50.000 0.00 0.00 40.21 2.52
3188 3288 2.657237 CTCCACGGCGACTTCCTT 59.343 61.111 16.62 0.00 0.00 3.36


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.